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Diff for /OpenXM/src/R/r-packages/note.txt between version 1.2 and 1.9

version 1.2, 2013/02/09 02:58:14 version 1.9, 2017/03/22 00:42:56
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 $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.1 2013/02/08 03:00:32 takayama Exp $  $OpenXM: OpenXM/src/R/r-packages/note.txt,v 1.8 2016/10/30 01:10:18 takayama Exp $
   
 See also OpenXM/src/hgm/note.txt  See also OpenXM/src/hgm/note.txt
   
Line 28  See also OpenXM/src/hgm/note.txt
Line 28  See also OpenXM/src/hgm/note.txt
     R CMD INSTALL hgm      R CMD INSTALL hgm
         R          R
         library(hgm)          library(hgm)
         You can check hgm.so3nc by hand.          You can check hgm.ncso3 by hand.
     R CMD REMOVE hgm      R CMD REMOVE hgm
         It is used to remove the test library.          It is used to remove the test library.
   
Line 39  See also OpenXM/src/hgm/note.txt
Line 39  See also OpenXM/src/hgm/note.txt
    or     or
     R CMD build --binary hgm  (perhaps, obsolete style)      R CMD build --binary hgm  (perhaps, obsolete style)
   
   (5) make copy-web-hgm
      hgm_x.yz.tar.gz
      [cran submit package] search ==> http://cran.r-project.org/submit.html
   
 * Notes.  * Notes.
     library.dynam()   shows a list of shared libraries loaded.      library.dynam()   shows a list of shared libraries loaded.
     dyn.load("hgm.so") can be used to load shared library by hand.      dyn.load("hgm.so") can be used to load shared library by hand.
     getwd() gets the current working directory.      getwd() gets the current working directory.
   
   
   * Undocumented functions which are removed temporary fro NAMESPACE. 2015.03.24
   export(hgm.so3nc)
   export(hgm.normalizingConstantOfFisherDistributionOnSO3)
   export(hgm.normalizingConstantOfOrthant)
   export(hgm.normalizingConstantOfBinghamDistribution)
   export(hgm.z.mleDemo)
   export(hgm.ssFB)
   
   
   * Check the memory leak by valgrind and by AddressSanitizer. 2015.04.01
   ** Valgrind
   apt-get install valgrind
   
   cat >>~/.valgrindrc
   --leak-check=full
   --track-origins=yes
   ctrl-D
   
   make clean
   R CMD check hgm --use-valgrind
   more hgm.Rcheck/hgm-Ex.Rout
   Example of an error (Note that there is no error message in *.log)
   ==14813== Conditional jump or move depends on uninitialised value(s)
   ==14813==    at 0xCA20170: mh_t (jack-n.c:1361)
     for (i=0; i<=M_m; i++) {
       -- snip
       serror = myabs((partial_sum[i]-partial_sum[i-1])/partial_sum[i-1]);
     }
     partial_sum[-1] is accessed!
   
   As to details, search "valgrind" in R-exts.pdf
   
   * R CMD check hgm --use-gct
   
   * Note on building R package: @s/2015/04/05-hgm-r-package-memo.txt
   
   ;;
   2016.02.15  testdata.
   c<-hgm.p2wishart(m=4,n1=50,n2=100,beta=c(1,2,4,8),q0=0.5,q=30,autoplot=1);
     output is wrong.
   c<-hgm.p2wishart(m=4,n1=50,n2=100,beta=c(1,2,4,8),q0=0.5,q=30,err=c(1e-30,1e-10),mode=c(1,1,0))
     output is correct.
   c<-hgm.p2wishart(m=4,n1=50,n2=100,beta=c(1,2,4,8),q0=0.5,q=30,err=c(1e-30,1e-10),autoplot=1)
     crashed, but by commented out todo in mh.c, it works. See @s/2016/02
   
   ;;
   http://kbroman.org/pkg_primer/pages/cran.html
   
   R CMD check hgm --as-cran
   
   
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